Related papers: Method for finding metabolic properties based on t…
Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to…
Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument…
The prevailing theory for metabolic scaling is based on area-preserved, space-filling fractal vascular networks. However, it's known both theoretically and experimentally that animals' vascular systems obey Murray's cubic branching law.…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
Production of energy is a foundation of life. Metabolic rate of organisms (amount of energy produced per unit time) generally increases slower than organisms' mass, which has important implications for life organization. This phenomenon,…
One of the most fundamental rules in metabolic ecology is the allometric equation, which is a power-law scaling that describes the connection between body measurements and body size. The biological dynamics of this essentially empirical…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
First, we briefly describe the general growth mechanism, which governs the growth of living organisms, and its mathematical representation, the growth equation. Using the growth equation, we compute growth curve for S. cerevisiae and show…
Obesity does not emerge abruptly; rather, it develops gradually over extended periods. The gradual progression often prevents early recognition of physiological changes until excess adiposity is established. A common belief is that weight…
A general simple theory for the interspecific allometric scaling is developed in the $d+1$-dimensional space ($d$ biological lengths and a physiological time) of metabolic states of organisms. It is assumed that natural selection shaped the…
Metabolism of living organisms is a foundation of life. The metabolic rate (energy production per unit time) increases slower than organisms' mass. When this phenomenon is considered across different species, it is called interspecific…
The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. Previous studies have utilized flux balance analysis and the maximum entropy method to predict…
Predicting cellular metabolic states is a central problem in biophysics. Conventional approaches, however, sensitively depend on the microscopic details of individual metabolic systems. In this Letter, we derived a universal linear…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…